2.21版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o channelNames <用户可见的变化,NChannelSet, *方法允许re-naming渠道o NChannelSet有效性要求所有assayDataElementNames()水平在varMetadata()美元通道。2.19版本的变化- - - - - - - - - - - - - - - - - - - - - - - -用户可见的变化o dimnames (), rownames (), colnames()和setter eSet-derived工作对象的变化版本2.17 - - - - - - - - - - - - - - - - - - - - - - - -用户可见的变化o l2e(),先前弃用,已经不复存在。o使所有对象已经在之前的发布周期已被移除。这包括geneNames、getExpData eList、reporterNames getBiocRepos,阅读。exprSet、updateOldMiame df2pD,阅读。pD,阅读。phenoData、exprData exprList, phenoData。2.11版本的变化- - - - - - - - - - - - - - - - - - - - - - -用户可见的变化o l2e弃用,使用“list2env”而不是o MIAME基类的搬到子类MIAxE虚拟类o MIAxE添加新特性虚拟类来保存试验元数据类2.7版本的变化- - - - - - - - - - - - - - - - - - - - - - -用户可见的变化阿秀,eSet-method总结protocolData,如果可用。o ' snpCall ' ' snpCallProbability SnpSet访问器补充道。BUG修复o ' selectSome回报短期因素字符()2.5版本的变化- - - - - - - - - - - - - - - - - - - - - - -用户可见的变化o ' protocolData槽添加到eSet类存储协议元数据存储在微阵列数据文件;可以访问由protocolData < - protocolData和设置。o ' sampleNames, NChannelSet-method时返回一个向量样本的名字每个频道都是相同的。 CHANGES IN VERSION 2.1 ---------------------- NEW FEATURES o 'makeDataPacakge' method for ExpressionSet now accepts a 'description' argument for the generated manual page. BUG FIXES o combine,matrix,matrix-method would record 'NA' for entries in the second matrix with niether rows nor columns present in the first. o openPDF now checks for NULL or zero-length pdfviewer option CHANGES IN VERSION 2.0 ---------------------- SIGNIFICANT USER-VISIBLE CHANGES o 'combine' on data.frame columns with mismatched levels causes a warning, rather than error. o updateObject does not warn about duplicating locked environment, unlesss verbose=TRUE NEW FEATURES o 'combine' now works to combine rows of ExpressionSet BUG FIXES o AnnotatedDataFrame 'show' listed additional varMetadata column names incorrectly when labelDescription was not the first. NEWLY DEFUNCT CLASSES, METHODS, FUNCTIONS, DATA SETS o Defunct S4 Classes 1) annotatedDataset - class definition still exits to support phenoData conversion 2) exprMatrix - removed class definition 3) exprSet - class definition still exists to allow conversion to ExpressionSet 4) phenoData - class definition still exists to allow conversion to AnnotatedDataFrame o Defunct Generics/Methods 1) addVarMetadataEntry - S4 generic definition removed 2) as.data.frame.exprSet - S3 method removed 3) convertVarLabels - S4 generic definition removed 4) eList - S4 methods remain with .Defunct messages 5) "eList<-" - S4 methods remain with .Defunct messages 6) exprs2excel - S4 generic definition removed 7) getExpData - S4 methods remain with .Defunct messages 8) geneNames - S4 methods remain with .Defunct messages 9) "geneNames<-" - S4 methods remain with .Defunct messages 10) getUnits - S4 generic definition removed 11) getVarMetadata - S4 generic definition removed 12) iter - S4 generic definition removed 13) reporterInfo - S4 generic definition removed 14) "reporterInfo<-" - S4 generic definition removed 15) reporterNames - S4 methods remain with .Defunct messages 16) "reporterNames<-" - S4 methods remain with .Defunct messages 17) split (for use with exprSet objects) - S4 generic definition removed 18) update2MIAME - S4 generic definition removed o Defunct functions 1) df2pD - function stub with .Defunct message 2) read.exprSet - function stub with .Defunct message 3) read.pD - function stub with .Defunct message 4) read.phenoData - function stub with .Defunct message 5) updateOldMiame - function stub with .Defunct message o Defunct data sets 1) bbsym 2) eset - use sample.ExpressionSet instead 3) golubMergeSub 4) sample.eSet - use sample.MultiSet instead 4) sample.exprSet.1 - use sample.ExpressionSet instead 5) sample.exprSet - use sample.ExpressionSet instead 6) SWPD 7) swrep